Dear Jastin Thanks your reply. as your email, I will generate velocity in NVT step with simulated annealing from 0 to 300K. What should be gen_temp value? Is 300 K correct?
Best Regards On Thursday, December 5, 2013 9:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 12/5/13 12:36 PM, kiana moghaddam wrote: > Dear GMX user > > I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at > 300 K in equilibration step. > I 'm very confused about velocity generation. > I use gen_vel= no in the first step (NVT) then generate velocity in the NPT > step at 300 K. After that, in production step I use gen_vel= no. Is my > process correct? > If you generate new velocities at the outset of NPT, it introduces new instability and basically negates any benefit of having done any prior equilibration. Preserve the velocities from NVT (via the .cpt file) when continuing to NPT. Rule of thumb: do not generate velocities for any step in the protocol that is not the very first one. There are exceptions, but they are generally rare. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
